whole genome sequencing from high molecular weight DNA using oxford nanopore sequencing from leaf tissue of Solanum tuberosum clone DM1S1
Genomic DNA for Oxford Nanopore Technologies (ONT) sequencing was isolated, purified and size selected, from greenhouse grown leaves of DM1S1 as described previously (Vaillancourt and Buell 2019). Short sequences were removed using the Ciruclomics Short Read Eliminator Kit (Circulomics, Baltimore, MD, Cat #SS-100-101-01). ONT DNA libraries were prepared using the ONT SQK-LSK109 Ligation Sequencing kit and sequenced on R9 ONT FLO-MIN106 Rev D flow cells. ONT gDNA reads were base-called using default parameters with Guppy v3.5.1 (https://community.nanoporetech.com/downloads) using a NVIDIA  V100 GPU with the dna_r9.4.1_450bps_hac.cfg configuration file.